We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...) transfer of modeling techniques from other fields. New and emerging views are characterized by different philosophies of nature, i.e. by different ontological and methodological assumptions and epistemic values and virtues. This results in a kind of conflict we call “epistemic competition” that manifests in two ways: On the one hand, opponents engage in mutual critique and defense of their fundamental assumptions. On the other hand, they compete for the acceptance and integration of the knowledge they provide by a broader scientific community. Despite an initial rhetoric of replacement, the views as well as the respective audiences come to be seen as more clearly distinct during the course of the debate. Hence, we observe—contrary to many other accounts of scientific change—that conflict results in the formation of new niches of research, leading to co-existence and perceived complementarity of approaches. Our model thus contributes to the understanding of the pluralization of the scientific landscape. (shrink)

The philosophical debate around the impact of machine learning in science is often framed in terms of a choice between AI and classical methods as mutually exclusive alternatives involving difficult epistemological trade-offs. A common worry regarding machine learning methods specifically is that they lead to opaque models that make predictions but do not lead to explanation or understanding. Focusing on the field of molecular biology, I argue that in practice machine learning is often used with explanatory aims. More specifically, I (...) argue that machine learning can be tightly integrated with other, more traditional, research methods and in a clear sense can contribute to insight into the causal processes underlying phenomena of interest to biologists. One could even say that machine learning is not the end of theory in important areas of biology, as has been argued, but rather a new beginning. I support these claims with a detailed discussion of a case study involving gene regulation by microRNAs. (shrink)

Systems biologists often distance themselves from reductionist approaches and formulate their aim as understanding living systems “as a whole.” Yet, it is often unclear what kind of reductionism they have in mind, and in what sense their methodologies would offer a superior approach. To address these questions, we distinguish between two types of reductionism which we call “modular reductionism” and “bottom-up reductionism.” Much knowledge in molecular biology has been gained by decomposing living systems into functional modules or through detailed studies (...) of molecular processes. We ask whether systems biology provides novel ways to recompose these findings in the context of the system as a whole via computational simulations. As an example of computational integration of modules, we analyze the first whole-cell model of the bacterium M. genitalium. Secondly, we examine the attempt to recompose processes across different spatial scales via multi-scale cardiac models. Although these models rely on a number of idealizations and simplifying assumptions as well, we argue that they provide insight into the limitations of reductionist approaches. Whole-cell models can be used to discover properties arising at the interfaces of dynamically coupled processes within a biological system, thereby making more apparent what is lost through decomposition. Similarly, multi-scale modeling highlights the relevance of macroscale parameters and models and challenges the view that living systems can be understood “bottom-up.” Specifically, we point out that system-level properties constrain lower-scale processes. Thus, large-scale modeling reveals how living systems at the same time are more and less than the sum of the parts. (shrink)

Even though complexity is a concept that is ubiquitously used by biologists and philosophers of biology, it is rarely made precise. I argue that a clarification of the concept is neither trivial nor unachievable, and I propose a unifying framework based on the technical notion of “effective complexity” that allows me to do justice to conflicting intuitions about biological complexity, while taking into account several distinctions in the usage of the concept that are often overlooked. In particular, I propose a (...) distinction between two kinds of complexity, “mechanical” and “emergent”, which can be understood as different ways of relating the effective complexity of mechanisms and of behaviors in biological explanations. I illustrate the adequacy of this framework by discussing different attempts to understand intracellular organization in terms of pathways and networks. My framework provides a different way of thinking about recent philosophical debates, for example, on the difference between mechanistic and topological explanations and about the concept of emergence. Moreover, it can contribute to a proper assessment of metascientific arguments that invoke biological complexity. (shrink)

- A recent debate has touched upon the question of whether diseases can be understood as dysfunctional mechanisms or whether there are "pathological" mechanisms that deserve to be investigated and explained independently (Nervi 2010; Moghaddam Taaheri 2011). Here I suggest that both views tell us something important about disease but that in many instances only a systemic view can shed light on the relationship between physiology and pathology. I provide examples from the literature in systems biology in support of my (...) position. As a result of my analysis, I conclude that a perspective narrowly focusing on mechanisms is insufficient if the goal is to get a comprehensive picture of disease. (shrink)

Occam’s razor refers to the idea that among competing explanations the simplest should be preferred. This principle has been understood and defended in different ways. Some systems biologists argue that traditional molecular biology is misguided because it relies on an unjustified application of Occam’s razor. I analyze which version of the principle is relevant in this context and ask whether the allegation stands up to scrutiny by looking at actual research. I defend the traditional approach by arguing that its use (...) of Occam’s razor is innocuous and by showing that systems biology heavily relies on considerations of simplicity as well. (shrink)

Systems biology is sometimes presented as providing a superior approach to the problem of biological complexity. Its use of ‘unbiased’ methods and formal quantitative tools might lead to the impression that the human factor is effectively eliminated. However, a closer look reveals that this impression is misguided. Systems biologists cannot simply assemble molecular information and compute biological behavior. Instead, systems biology’s main contribution is to accelerate the discovery of mechanisms by applying models as heuristic tools. These models rely on a (...) variety of idealizing and simplifying assumptions in order to be efficient for this purpose. The strategies of systems biologists are similar to those of experimentalists in that they attempt to reduce the complexity of the discovery process. Analyzing and comparing these strategies, or ‘heuristics’, reveals the importance of the human factor in computational approaches and helps to situate systems biology within the epistemic landscape of the life sciences. (shrink)

Cancers rely on multiple, heterogeneous processes at different scales, pertaining to many biomedical fields. Therefore, understanding cancer is necessarily an interdisciplinary task that requires placing specialised experimental and clinical research into a broader conceptual, theoretical, and methodological framework. Without such a framework, oncology will collect piecemeal results, with scant dialogue between the different scientific communities studying cancer. We argue that one important way forward in service of a more successful dialogue is through greater integration of applied sciences (experimental and clinical) (...) with conceptual and theoretical approaches, informed by philosophical methods. By way of illustration, we explore six central themes: (i) the role of mutations in cancer; (ii) the clonal evolution of cancer cells; (iii) the relationship between cancer and multicellularity; (iv) the tumour microenvironment; (v) the immune system; and (vi) stem cells. In each case, we examine open questions in the scientific literature through a philosophical methodology and show the benefit of such a synergy for the scientific and medical understanding of cancer. (shrink)

In the present paper, it is shown that Kant in his theory of fine art from the Critique of Aesthetic Judgment proves to be a proponent of aesthetic cognitivism, according to which art is, first, a source of non-trivial knowledge and, second, this knowledge also has aesthetic relevance. This issue has been raised several times in the recent research literature, but has not been substantiated, or only briefly. Central to this is Kant's conception of aesthetic ideas, with which fine art (...) symbolizes intellectual ideas of various genesis and with which his theory of art acquires a content-aesthetic dimension. Discussing recent research literature, an interpretation for the conception of aesthetic ideas and the accompanying expressive dimension of fine art is offered in a first part. Based on this, it will be shown in a second part that Kant hereby proves to be a representative of aesthetic cognitivism; this is shown by the fact that his theory of art confirms both criteria of aesthetic cognitivism. (shrink)

Should a theory of meaning state what sentences mean, and can a Davidsonian theory of meaning in particular do so? Max Ko¨lbel answers both questions affirmatively. I argue, however, that the phenomena of non-homophony, non-truth-conditional aspects of meaning, semantic mood, and context-sensitivity provide prima facie obstacles for extending Davidsonian truth-theories to yield meaning-stating theorems. Assessing some natural moves in reply requires a more fully developed conception of the task of such theories than Ko¨lbel provides. A more developed conception is also (...) required to defend his positive answer to the first question above. I argue that, however Ko¨lbel might elaborate his position, it can’t be by embracing the sort of cognitivist account of Davidsonian semantics to which he sometimes alludes. (shrink)

This authoritative volume provides a comprehensive road map of the important and rapidly growing field of emotion regulation.

"Evidence of a flight from reason is as old as human record-keeping: the fact of it certainly goes back an even longer way. Flight from science specifically, among the forms of rational inquiry, goes back as far as science itself... But rejection of reason is now a pattern to be found in most branches of scholarship and in all the learned professions."--from the introduction In the widely acclaimed Higher Superstition: The Academic Left and Its Quarrels with Science, Paul R. (...) class='Hi'>Gross and Norman Levitt offered a spirited response to the "science bashers," raising serious questions about the growing criticism of scientific practice from humanists and social scientists on the academic left. Now, in The Flight from Science and Reason, Gross and Levitt are joined by Martin W. Lewis to bring together a diverse and distinguished group of scholars, scientists, and experts to engage these questions from a wide variety of perspectives. The authors take on critics of science whose views range from moderate to extreme, from social constructivists to deconstructionists, from creationists and feminists to Afro-centrists. They discuss the rise of "alternative medicine" and radical environmentalism (here skewered as "ecosentimentalism"). They explain why the "uncertainty principle" does not work as a metaphor for ambiguity, and why "chaos theory" cannot be invoked without an understanding of mathematics. Throughout, they grapple with the paradox inherent in arguing with opponents who contend that reason itself, and thus logic, is suspect. Distributed for the New York Academy of Sciences. (shrink)

Alan Gross applies the principles of rhetoric to the interpretation of classical and contemporary scientific texts to show how they persuade both author and audience. This invigorating consideration of the ways in which scientists--from Copernicus to Darwin to Newton to James Watson--establish authority and convince one another and us of the truth they describe may very well lead to a remodeling of our understanding of science and its place in society.

Catholic thinkers generally agree that artificial womb technology (AWT) would be permissible in cases of partial ectogenesis to assist severely premature infants, but there is substantially more debate concerning whether AWT could be used to save frozen embryos, which are the result of in vitro fertilization (IVF). In many cases, these embryos have been abandoned and left in a permanently cryogenic state, which is an affront to their human dignity. While AWT would allow people to adopt these embryos and give (...) them an opportunity to develop, it gives rise to serious concerns over the possibility of scandal and the potential for cooperation in evil. Therefore, the author argues that even though AWT may one day represent a solution to this tragedy, it is currently not a morally licit answer, given the widespread use and approval of IVF in our culture. (shrink)

This is a book review of: Robert B. Brandom, Articulating Reasons: An Introduction to Inferentialism. Cambridge: Harvard University Press, 2000. Pp. 230.

Decentralized biobanking “de-bi” applies blockchain technology and web3 values to embed the procedural principles of transparency, accountability, and inclusion into the biomedical research ecosyst...

Nick Shea’s Representation in Cognitive Science commits him to representations in perceptual processing that are about probabilities. This commentary concerns how to adjudicate between this view and an alternative that locates the probabilities rather in the representational states’ associated “attitudes”. As background and motivation, evidence for probabilistic representations in perceptual processing is adduced, and it is shown how, on either conception, one can address a specific challenge Ned Block has raised to this evidence.

Comment on Dean Pettit, who replies in same issue.

Does perceptual consciousness require cognitive access? Ned Block argues that it does not. Central to his case are visual memory experiments that employ post-stimulus cueing—in particular, Sperling's classic partial report studies, change-detection work by Lamme and colleagues, and a recent paper by Bronfman and colleagues that exploits our perception of ‘gist’ properties. We argue contra Block that these experiments do not support his claim. Our reinterpretations differ from previous critics' in challenging as well a longstanding and common view of visual (...) memory as involving declining capacity across a series of stores. We conclude by discussing the relation of probabilistic perceptual representations and phenomenal consciousness. (shrink)

Zenon Pylyshyn argues that cognitively driven attentional effects do not amount to cognitive penetration of early vision because such effects occur either before or after early vision. Critics object that in fact such effects occur at all levels of perceptual processing. We argue that Pylyshyn’s claim is correct—but not for the reason he emphasizes. Even if his critics are correct that attentional effects are not external to early vision, these effects do not satisfy Pylyshyn’s requirements that the effects be direct (...) and exhibit semantic coherence. In addition, we distinguish our defense from those found in recent work by Raftopoulos and by Firestone and Scholl, argue that attention should not be assimilated to expectation, and discuss alternative characterizations of cognitive penetrability, advocating a kind of pluralism. (shrink)

The eminent and award-winning historian Robert A. Gross presents his long-awaited, immersive journey through Concord in the age of Emerson and Thoreau.

A survey of innateness in cognitive science, focusing on (1) what innateness might be, and (2) whether concepts might be innate.

According to cognitivist truth-theoretic accounts of semantic competence, aspects of our linguistic behavior can be explained by ascribing to speakers cognition of truth theories. It's generally assumed on this approach that, however much context sensitivity speakers' languages contain, the cognized truththeories themselves can be adequately characterized context insensitively—that is, without using in the metalanguage expressions whose semantic value can vary across occasions of utterance. In this paper, I explore some of the motivations for and problems and consequences of dropping this (...) assumption. (shrink)

One of the most fundamental distinctions in the field of emotion is the distinction between emotion generation and emotion regulation. This distinction fits comfortably with folk theories, which view emotions as passions that arise unbidden and then must be controlled. But is it really helpful to distinguish between emotion generation and emotion regulation? In this article, we begin by offering working definitions of emotion generation and emotion regulation. We argue that in some circumstances, the distinction between emotion generation and emotion (...) regulation is indeed useful. We point both to citation patterns, which indicate that researchers from across a number of sub-areas within psychology are making this distinction, and to empirical studies, which indicate the utility of this distinction in many different research contexts. We then consider five ways in which the distinction between emotion generation and emotion regulation can be problematic. We suggest that it is time to move beyond debates about whether this distinction is useful to a more specific consideration of when and in what ways this distinction is useful, and in this spirit, we offer recommendations for future research. (shrink)

We bring together recent discussions on data capitalism and biocapitalization by studying value flows in consumer genomics firms—an industry at the intersection between health care and technology realms. Consumer genomics companies market genomic testing services to consumers as a source of fun, altruism, belonging and knowledge. But by maintaining a multisided or platform business model, these firms also engage in digital capitalism, creating financial profit from data brokerage. This is a precarious balance to strike: If these companies’ business models consist (...) of assetizing the pool of genomic data that they assemble, then part of their work has to revolve around obscuring to consumers any uncertainties that would potentially impinge on these processes of assemblage. We reflect on the nature of these practices and the market relationships that enable them, and we relate this reflection to debates around alternative market arrangements that would potentially mitigate the extractive tendencies of these and other digital health firms. (shrink)

One of the most fundamental distinctions in the field of emotion is the distinction between emotion generation and emotion regulation. This distinction fits comfortably with folk theories, which view emotions as passions that arise unbidden and then must be controlled. But is it really helpful to distinguish between emotion generation and emotion regulation? In this article, we begin by offering working definitions of emotion generation and emotion regulation. We argue that in some circumstances, the distinction between emotion generation and emotion (...) regulation is indeed useful. We point both to citation patterns, which indicate that researchers from across a number of sub-areas within psychology are making this distinction, and to empirical studies, which indicate the utility of this distinction in many different research contexts. We then consider five ways in which the distinction between emotion generation and emotion regulation can be problematic. We suggest that it is time to move beyond debates about whether this distinction is useful to a more specific consideration of when and in what ways this distinction is useful, and in this spirit, we offer recommendations for future research. (shrink)

Linguistic intuitions are a central source of evidence across a variety of linguistic domains. They have also long been a source of controversy. This chapter aims to illuminate the etiology and evidential status of at least some linguistic intuitions by relating them to error signals of the sort posited by accounts of on-line monitoring of speech production and comprehension. The suggestion is framed as a novel reply to Michael Devitt’s claim that linguistic intuitions are theory-laden “central systems” responses, rather than (...) endorsed outputs of a modularized language faculty (the “Voice of Competence”). Along the way, it is argued that linguistic intuitions may not constitute a natural kind with a common etiology; and that, for a range of cases, the process by which intuitions used in linguistics are generated amounts to little more than comprehension. (shrink)

Theories of consciousness divide over whether perceptual consciousness is rich or sparse in specific representational content and whether it requires cognitive access. These two issues are often treated in tandem because of a shared assumption that the representational capacity of cognitive access is fairly limited. Recent research on working memory challenges this shared assumption. This paper argues that abandoning the assumption undermines post-cue-based “overflow” arguments, according to which perceptual conscious is rich and does not require cognitive access. Abandoning it also (...) dissociates the rich/sparse debate from the access question. The paper then explores attempts to reformulate overflow theses in ways that don’t require the assumption of limited capacity. Finally, it discusses the problem of relating seemingly non-probabilistic perceptual consciousness to the probabilistic representations posited by the models that challenge conceptions of cognitive access as capacity-limited. (shrink)

Princess Diana’s death was a tragedy that provoked mourning across the globe; the death of a homeless person, more often than not, is met with apathy. How can we account for this uneven distribution of emotion? Can it simply be explained by the prevailing scientific understanding? Uncovering a rich tradition beginning with Aristotle, _The Secret History of Emotion_ offers a counterpoint to the way we generally understand emotions today. Through a radical rereading of Aristotle, Seneca, Thomas Hobbes, Sarah Fielding, and (...) Judith Butler, among others, Daniel M. Gross reveals a persistent intellectual current that considers emotions as psychosocial phenomena. In Gross’s historical analysis of emotion, Aristotle and Hobbes’s rhetoric show that our passions do not stem from some inherent, universal nature of men and women, but rather are conditioned by power relations and social hierarchies. He follows up with consideration of how political passions are distributed to some people but not to others using the Roman Stoics as a guide. Hume and contemporary theorists like Judith Butler, meanwhile, explain to us how psyches are shaped by power. To supplement his argument, Gross also provides a history and critique of the dominant modern view of emotions, expressed in Darwinism and neurobiology, in which they are considered organic, personal feelings independent of social circumstances. The result is a convincing work that rescues the study of the passions from science and returns it to the humanities and the art of rhetoric. (shrink)

The sublime evokes our awe, our terror, and our wonder. Applied first in ancient Greece to the heights of literary expression, in the 18th-century the sublime was extended to nature and to the sciences, enterprises that viewed the natural world as a manifestation of God's goodness, power, and wisdom. In The Scientific Sublime, Alan Gross reveals the modern-day sublime in popular science. He shows how the great popular scientists of our time--Richard Feynman, Stephen Hawking, Steven Weinberg, Brian Greene, Lisa (...) Randall, Rachel Carson, Stephen Jay Gould, Steven Pinker, Richard Dawkins, and E. O. Wilson--evoke the sublime in response to fundamental questions: How did the universe begin? How did life? How did language? These authors maintain a tradition initiated by Joseph Addison, Edmund Burke, Immanuel Kant, and Adam Smith, towering 18th-century figures who adapted the literary sublime first to nature, then to science--though with one crucial difference: religion has been replaced wholly by science. In a final chapter, Gross explores science's attack on religion, an assault that attempts to sweep permanently under the rug two questions science cannot answer: What is the meaning of life? What is the meaning of the good life? (shrink)

Asymmetric conflict is changing the way that we practise and think about war. Torture, rendition, assassination, blackmail, extortion, direct attacks on civilians, and chemical weapons are all finding their way to the battlefield despite longstanding international prohibitions. This book offers a practical guide for policy makers, military officers, students, and others who ask such questions as: do guerillas deserve respect or long jail sentences? Are there grounds to torture guerillas for information or assassinate them on the battlefield? Is there room (...) for nonlethal weapons to subdue militants and safeguard the lives of noncombatants? Who are noncombatants in asymmetric war? What is the status of civilians who shelter and aid guerillas? And, do guerillas have any right to attack civilians, particularly those who aid and shelter members of the stronger army? If one side can expand the scope of civilian vulnerability, then why can't the other? (shrink)

Unlike most Western nations, Israel does not recognize full separation of church and state but seeks instead a gentle fusion of Jewish and democratic values. Inasmuch as important religious norms such as sanctity of life may clash with dignity, privacy, and self-determination, conflicts frequently arise as Israeli lawmakers, ethicists, and healthcare professionals attempt to give substance to the idea of a Jewish-democratic state. Emerging issues in Israeli bioethics—end-of-life treatment, fertility, genetic research, and medical ethics during armed conflict—highlight this conflict vividly.

Social scientists have traditionally attempted to avoid extending strategies for acquiring experimental knowledge to the sphere of the social. Bruno Latour, however, has introduced a notion of the collective experiment, an experiment conducted by and with us all. In this short paper I seek to explore, by way of elucidating the talk of collective experiments, that Latour's notion has long since existed in the theory and practice of ecological design and restoration. Practitioners in ecological restoration projects find themselves in a (...) situation of double contingency, since neither do they know how nature will respond to their intervention nor is their interpretation of these responses already certain. Experimental practice in society then becomes the proceduralization of this contingency. (shrink)

Because the goal of military medicine is salvaging the wounded who can return to duty, military medical ethics cannot easily defend devoting scarce resources to those so badly injured that they cannot return to duty. Instead, arguments turn to morale and political obligation to justify care for the seriously wounded. Neither argument is satisfactory. Care for the wounded is not necessary to maintain an army's morale. Nor is there any moral or logical connection between the right to health care (a (...) universal human right) and the duty to defend one's nation (a local political duty). Once badly wounded, soldiers enjoy the same right to medical care as any similarly ill or injured individual. National health care systems grasp this point and offer few additional health care benefits to veterans. In the United States, however, lack of universal health coverage skews the debate to focus on special entitlements for veterans without considering the health care rights that other citizens enjoy. (shrink)

Can one combine Davidsonian semantics with a deflationary conception of truth? Williams argues, contra a common worry, that Davidsonian semantics does not require truth-talk to play an explanatory role. Horisk replies that, in any event, the expressive role of truth-talk that Williams emphasizes disqualifies deflationary accounts—at least extant varieties—from combination with Davidsonian semantics. She argues, in particular, that this is so for Quine's disquotationalism, Horwich's minimalism, and Brandom's prosententialism. I argue that Horisk fails to establish her claim in all three (...) cases. This involves clarifying Quine’s understanding of a purely referential occurrence; explaining how Davidsonians can avail themselves of a syntactic treatment of lexical ambiguity; and correcting a common misreading of Brandom (answering along the way an objection offered by Künne as well). (shrink)

Responsible citizens are expected to combine ethical judgement with judiciously exercised social activism to preserve the moral foundation of democratic society and prevent political injustice. But do they? Utilizing a research model integrating insights from rational choice theory and cognitive developmental psychology this book carefully explores three exemplary cases of morally inspired activism: Jewish rescue in wartime Europe, abortion politics in the United States, and peace and settler activism in Israel. From all three analyses a single conclusion emerges: the most (...) politically competent individuals are, most often, the least morally competent. This is the central paradox of political morality. These findings cast doubt on strong models of political morality characterized by enlightened moral reasoning and concerted political action while affirming alternative weak models that fuse activism with sectarian moral interests. They provide empirical support to further upend the liberal vision of democratic character, education, and society. (shrink)

If rhetoric is the art of speaking, who is listening? In Being-Moved, Daniel M. Gross provides an answer, showing when and where the art of speaking parted ways with the art of listening-and what happens when they intersect once again. Much in the history of rhetoric must be rethought along the way. And much of this rethinking pivots around Martin Heidegger's early lectures on Aristotle's Rhetoric, where his famous topic, Being, gives way to being-moved. The results, Gross goes (...) on to show, are profound. Listening to the gods, listening to the world around us, and even listening to one another in the classroom-all of these experiences become different when rhetoric is reoriented from the voice to the ear. (shrink)